linkSet

[GilbertHan1011]

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• Repository: https://github.com/GilbertHan1011/linkSet

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[bioc-issue-bot]

Hi @GilbertHan1011

Thanks for submitting your package. We are taking a quick
look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: linkSet
Title: Base Classes for Storing Genomic Link Data
Version: 0.99.0
Authors@R: 
    person("Gilbert", "Han", , "[email protected]", role = c("aut", "cre"),
 comment = c(ORCID = "0009-0000-0293-2467"))
Description: The goal of linkSet is to provide tools for working with gene-enhancer interactions, which is commonly seen in HiC, PC-HiC, and single-cell ATAC-seq data analysis. 
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends: 
    GenomicRanges,
    R (>= 2.10)
Imports: 
    methods,
    Matrix,
    S4Vectors,
    IRanges,
    GenomeInfoDb,
    BiocGenerics,
    Organism.dplyr,
    InteractionSet,
    ggplot2,
    patchwork,
    scales,
    dplyr,
    foreach,
    iterators,
    stats,
    rlang,
    MASS,
    data.table
Suggests: 
    knitr,
    rmarkdown,
    testthat,
    TxDb.Mmusculus.UCSC.mm10.knownGene,
    org.Mm.eg.db,
    GenomicFeatures,
    gamlss,
    gamlss.tr
Collate: class.R AllGenerics.R getset.R
        methods.R annotate.R distance.R formatConverter.R 
        linkSet-package.R GRange_method.R test_helper.R
        visualization.R count.R statical.R
biocViews: Software, HiC, DataRepresentation
URL: https://github.com/GilbertHan1011/linkSet, https://gilberthan1011.github.io/linkSet, https://gilberthan1011.github.io/linkSet/
BugReports: https://github.com/GilbertHan1011/linkSet/issues/new
LazyData: true
VignetteBuilder: knitr

[lshep]

We prefer to have a clean upload to Bioconductor. Please remove pkgdown
directories from default branch until uploaded to Bioconductor.

Please also provide an inst/scripts directory that describes how the data
in inst/extdata was generated. It can be code, pseudo-code, or text but
should minimally list any source or licensing information.

for your vignette hic_workthrough, you don't have to download the
file. rtracklayer will use a remote url.

> file_url <- c("http://www.enhanceratlas.org/data/download/enhancer/mm/Embryo_body.bed")
> enhancer <- rtracklayer::import(file_url, format="BED")
> enhancer
GRanges object with 3726 ranges and 1 metadata column:
         seqnames              ranges strand |             name
            <Rle>           <IRanges>  <Rle> |      <character>
     [1]     chr1     4561881-4562150      * |  13.507493224644
     [2]     chr1   12683361-12683590      * | 14.0682990384515
     [3]     chr1   12785091-12785750      * | 12.2266622787328
     [4]     chr1   14496641-14497000      * | 16.1891332694206
     [5]     chr1   24202811-24203230      * | 11.8691663511038
     ...      ...                 ...    ... .              ...
  [3722]     chrX 166440901-166446910      * | 11.2914586799194
  [3723]     chrY     1788141-1793200      * | 14.1421609105058
  [3724]     chrY     2850391-2872320      * | 23.6283376743297
  [3725]     chrY     2875631-2894080      * | 39.6196744784028
  [3726]     chrY     2894111-2901180      * | 14.9351349382787
  -------
  seqinfo: 21 sequences from an unspecified genome; no seqlengths

you extensive use GInteraction in the vignette and provide the conversion method which is great. Can you explain a little more why that class or an extension of that class was not sufficient and the necessity to create the new class.

[GilbertHan1011]

@lshep Thank you for your thorough review and valuable suggestions. I have made several improvements based on your feedback:

1. The pkgdown directories have been removed from the default branch for better organization.
2. I have regenerated the data in inst/extdata and created a script to document the data generation process, making it more transparent and reproducible.
3. Remote URLs are now used in the hic_workthrough vignette to improve accessibility.
4. I have written a blog post explaining the limitations of the GInteraction class in the InteractionSet package and why additional functionality was needed. I hope this helps clarify the motivation behind this work.

These changes should make the package more user-friendly and better documented. I appreciate your guidance in helping improve this project.

[bioc-issue-bot]

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[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "ERROR".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): linkSet_0.99.1.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/linkSet to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: bdf62a667f48c5a61d07f08d71f921f7bf445be5

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "ERROR".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): linkSet_0.99.2.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/linkSet to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 49af01b7485d26530e50d72607598d13be1745e0

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "WARNINGS".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): linkSet_0.99.3.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/linkSet to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

A reviewer has been assigned to your package for an indepth review.
Please respond accordingly to any further comments from the reviewer.

[svalvaro]

Hi @GilbertHan1011 I browsed quickly through the repo, (I'll do an deeper review when you check the following things).

1. Please add Bioconductor installation instructions in the readme and vignettes.
2. I noticed many .pngs favicons etc in the docs folder, are you using all of them?

[GilbertHan1011]

Hi @svalvaro, thank you for your review and feedback.

1. I have added the Bioconductor installation instructions to both the README and the vignettes.
2. The .png files are automatically generated by the pkgdown package. You can see similar examples in other packages, such as decoupleR. However, I agree that including the docs folder in the master branch is not ideal. Therefore, I have removed this folder from GitHub. I appreciate your suggestion!